Simulations and Molecular Modeling Research Unit (SMM)

Building Capacity Through Collaboration

The Simulation and Molecular Modelling (SMM) Unit at the University of Warith Al-Anbiyaa has played a central role in nurturing a new wave of scientific talent in Iraq. Through a series of hands-on training workshops held over the past two years, the unit has introduced students, young researchers, and academics to modern tools in computational chemistry and simulation-based science. These workshops filled a long-standing gap in scientific training, particularly in areas where access to traditional laboratory resources is limited.

Alongside these efforts, SMM has secured meaningful partnerships with universities and research groups abroad. Letters of collaboration have been exchanged to support staff development, knowledge sharing, and joint research projects. These partnerships are helping to place Iraq's researchers on the global scientific map, creating long-term pathways for innovation and cooperation.

Photos highlight the enthusiasm and engagement of workshop participants, reflecting a growing appetite for digital science in the region. Together, these training activities and international collaborations demonstrate a serious and practical commitment to scientific development — one that's already beginning to make a lasting impact.

SMM researchers develop and apply computer programs to answer key questions in several scientific sections:

1-      Computer-Aided Drug Discovery (CADD)

CADD is a powerful tool in modern drug discovery which employs computer algorithms to find the correct composition of a drug, develop the drug, and analyze its performance on a biological target. CADD techniques have been extremely successful in accelerating the pace of designing of new efficient drugs and medications which has helped in treating various kinds of diseases and ailments ranging from AIDS to glaucoma.

We are collaborating with Professor Reynisson Research Group (Keele University, UK) to work on exploring the nature of known drug space (KDS) and its application as a navigational tool in chemical space.

2-      Bioinformatics:

In this section, we undertake the task of mapping networks of protein interactions, aiming to decipher intricate biochemical pathways and identify crucial points for potential intervention. This approach enables us to gain a quantitative and visual understanding of the nature of substrate-enzyme interactions. We place significant emphasis on conducting comparative analyses, which aim to elucidate both common themes and differences in the structure-function relationships among protein families. This analysis facilitates a deeper comprehension of complex biological phenomena, rooted in fundamental biological and chemical principles.

To achieve these objectives, we perform detailed investigations of peptide interactions in their isomeric forms, employing QM/MM calculations to examine different structural snapshots. This analysis enables us to identify key contacts and residues that may hold significant importance and should be included in the subsequent QM/MM calculations. Our research efforts are part of a collaborative project with the Professor Zoltán Gáspári’s Group from Pázmány Péter Catholic University, Hungary. The primary focus of this collaboration lies in systematically and comprehensively exploring the interdependence of intramolecular motions, catalysis, and regulation in enzymes. Through these endeavors, we aim to contribute to the advancement of knowledge in the field of protein structure-function relationships and pave the way for a better understanding of biological processes at the molecular level.

3-      Medical Radio-Chemistry.

We are working in collaboration with experiments Prof. Constantin Mamatt in Germany and Prof. Sandra Luber at the University of Zurich, Switzerland on designing a macro-ligands that can help to collect the radio-active elements from the patients. The radio active element such as Barium and Radium element could be collected from the patients body by calixcrowns that have multi-dentate coordination sites, the ultimate aim to design the safest, cheaper, and most effective medicine to recover the traces of element from the body tissues.

4-      Nanotechnology:

We use cutting-edge computational approaches to investigate the environmental and sustainability applications for several selected nanoclusters (Au, Pd, Cu, Ru, Pt, Ir, and Sc) and their nanoalloys (mixtures of two metals). The adsorption of the nanoclusters on different functional surfaces is considered as well as their reactivity towards certain small molecules (e.g. CO, CO2, SO2, and H2).

This research is being carried out in collaboration with four world-class experimental and theoretical research groups: Lievens group (K. U. Leuven in Belgium), Fielicke group (T. U. Berlin in Germany), Gaston group (U. Auckland in New Zealand), and Johnston group (U. Birmingham in UK).

5-      2D Materials for Gas Sensing Technology

The monitoring of toxic gases has emerged as a prominent concern due to the escalation of severe environmental issues that pose significant threats to global public health security. Consequently, the development of highly sensitive gas detectors has become imperative in the pursuit of controlling air quality. The effectiveness of gas sensors fundamentally relies on their sensing material, the core component responsible for gas detection. Critical attributes of sensing materials include selectivity, response, and stability. An ideal gas sensor should possess qualities such as affordability, the ability to detect low concentrations of target gases, high response sensitivity, long-term stability, and operation at ambient room temperature. Hence, the scientific community faces a substantial challenge in developing efficient and effective gas-sensing devices for monitoring hazardous and toxic gases.

In our research, we primarily utilize theoretical calculations to investigate the interactions between gas molecules and 2D sensing materials. This approach enables us to devise novel ideas for enhancing the gas-sensing performance of such materials. Through fruitful collaborations with esteemed experts in the field, namely Prof. Abbas H. Abo Nasria from the Department of Physics at the University of Kufa and Dr. Nicola Seriani from the Abdus Salam International Centre for Theoretical Physics (ICTP) in Italy, we aim to improve the gas sensing properties of 2D nanomaterials. Our investigations focus on techniques such as defect functionalization, heterojunctions, external electric field modulation, and light irradiation to elevate the gas-sensing capabilities of these materials.

6-      Hydrogen Storage Technology

To address the challenges posed by the intermittence of renewable energies, the depletion of fossil fuels, and climate-related issues, the adoption of hydrogen as an energy vector appears to be a promising solution. Hydrogen offers an excellent means of storing energy on a large scale for extended durations, making it suitable for diverse applications such as mobility, heat generation, and industrial processes, all while having a negligible impact on the carbon footprint. It can be utilized in both mobile and stationary applications through fuel cells or direct combustion. However, effective utilization of hydrogen hinges on its storage, which presently remains a critical issue.

Developing a viable medium for hydrogen storage at moderate temperature and pressure is of utmost importance. Among potential solutions, solid-state storage in nanoporous two-dimensional and three-dimensional materials, such as graphene, aerogels, and MXenes structures, holds promise for achieving satisfactory gravimetric and volumetric densities. Nevertheless, in-depth fundamental research is indispensable to fully comprehend the potential of this technology and to facilitate its practical implementation.

In our ongoing research, we are employing advanced computational techniques, including Density Functional Theory (DFT) and Molecular Dynamic (MD) Simulation methods, to rationally design functional nanomaterials that exhibit efficient energy storage capabilities. This investigation aims to contribute significantly to the advancement of hydrogen storage technology, paving the way for sustainable and eco-friendly energy solutions in the future.

 We are working in collaboration with Professor Tanveer Hussain (U. Western Australia) on exploring the mechanical response and reactivity of a 2D-material for hydrogen storage application.

7-      Water Splitting Catalysis.

We use computational chemistry methodologies to understand the water splitting catalysis. We mimic the nature PSII complexes to design artificial water splitting catalysis that are known for oxygen-evolving catalysis OEC.

8-       Single Molecular Magnets:

The aim of such studies is to design the smallest magnets in the world, these magnets consist of single molecules that will revolutionize the future memory and spintronics industry. We are working in collaboration with Professor John McGrady at the University of Oxford, UK and Professor Yannis Sanakis at the Democritos Research Institute on designing single molecular clusters that have a unique magnetic properties.

9-      Genetic Algorithms for Chemistry

Over the past two decades, there have been significant developments of sophisticated search algorithms, in particular, genetic algorithms (GAs). GAs have been used to predict the structures (and hence the physical and chemical properties) of mixed-metal “nanoalloy” clusters, with an emphasis on subnanometer clusters, via the coupling of the GA with electronic structure calculations, particularly density functional theory. In collaboration with a number of theoreticians, we also employ different computational approaches and high-performance computing architectures to develop our GAs codes.